Standard Operating Procedures for manufacturing, screening and analysis of TopoChips
BiS, Biointerface Science in Regenerative Medicine at the Department of Biomedical Engineering, Eindhoven University of Technology
BiS, Biointerface Science in Regenerative Medicine at the Department of Biomedical Engineering, Eindhoven University of Technology
In this section you can find the Standard Operating Procedures we have developed over the years to enable TopoChip screening. You will find SOPs on design and manufacturing of TopoChips using hot embossing, there are SOPs on assay development, on high content imaging but we also provide SOPs on the data processing machine learning protocols
1. Fabrication
1.2 Oxygen plasma treatment
This SOP describes how to perform oxygen plasma treatment to the Si
molds, Ormomolds and polymer substrates with the TopoChip imprints
1.3 Silanization of Si wafer master mould and Ormomould
This SOP describes how to perform silane treatment to the Si wafer
TopoChip and Ormomould to increase hydrophobicity
1.4 PDMS TopoChip Inter-mould Production from the Si Master mould
This SOP describes how to produce a PDMS mould from the master Si
mould as a mid-step to make an OrmoMould (SOP 1.5)
1.5 OrmoMould Fabrication for Polymer Imprinting
This SOP describes how to fabricate an OrmoMould using OrmoStamp®
to produce a hard mould with various topographies to imprint
polymers via hot embossing
1.6 Polymer TopoChip production by hot embossing
This SOP describes how to imprint TopoChips (or any other
topographies) on polymer substrates using an OrmoMould via the hot
embossing method.
2. Bioassays
2.1 Sterilization of TopoChip
This SOP describes how to sterilize the TopoChip using 70 % ethanol.
2.2 Cell seeding onto the TopoChip
This SOP describes how cells are seeded onto the TopoChip
2.3 Immunofluorescence staining of TopoChips
This SOP describes how to do an immunofluorescence staining of
a TopoChip. It can be adapted to the antibodies that are used for
specific screen.
3. Imaging
3.1 Imaging of TopoChip with Nikon Ti2 microscope
This SOP describes how to scan a whole TopoChip with the Nikon Ti2
system
4. Analysis
4.1 Installing all necessary software and setup environment
This SOP describes installing the software that is required to run
TopoChip Data analysis templates and provides references for
learning materials
4.2 Images analysis workflow
This SOP describes cropping of the images and how to run the
CellProfiler analysis.
4.3 Aligning Image Analysis Results With TopoMap
This SOP describes the steps required to aligning image analysis
results with TopoMap.
4.4 Identification and removal of TopoUnit outliers
This SOP describes the steps that are required to identify,
visualize, and remove TopoUnit outliers.
4.5 Rank surfaces to feature of interest
This SOP describes the steps that are required to rank the
surfaces based on the performance in the screen.
4.6 Training a machine learning model from the TopoChip ranking data
This SOP describes the typical steps that are required to train and
explain machine learning model from the TopoChip ranking data.
Content